Alterations
by QuestionDeca
Summary: The Ark has fallen and things have changed. Now Sonic and co. must deal with a whole new world, whole new problems, and a blurred line between friend, foe, and themselves.
1. Introductions to a New World

**SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
  
**Introductions to a ******New World**** (or ****the End, or Beginning? Version:2)******

**Inside the Space Colony (5 minutes after time to impact):  
  
**

Everyone in the lab turned as the doors hissed open, behind them stood Sonic, hanging his head.  
  


Rouge spoke quickly, "Shadow, is he…" but Rouge was interrupted by another voice, coming from Sonic's right.  
  


"I'm fine, I had run out of energy but Sonic was able to get us both out of there in time." Shadow spoke as he walked up beside Sonic, weariness showing in his eyes.  
  


Sonic walked in the promptly sat himself down against a wall, "Man, I'm beat," he pauses to catch his breath (AN: GASP) then asks, "So what happens next?"  
  


As the last word escapes his lips a new alarm none of them had heard before cries out throughout the Space Colony.  
  


Eggman quickly moves to the room's terminal, "Tails, quickly get over here, I'll need you run a diagnostic on the colony's integrity while I run through the systems to find out what is wrong."  
  


As the two quickly typed, Rouge and Amy walked up to the two.  
  


Amy arrives first and asks Tails a question, "What does the colony's Integrity mean?"

Tails looked quickly at Amy before turning back and giving his answer, "The colony's integrity is how strong it's inner and outer walls are, if the inner walls weaken parts of the colony could collapse in on themselves while if the outer walls weaken then the entire colony could be depressurized and everything and one would be sucked out into space."  
  


Tails' reply frightens Amy but she quickly buries her fear and tries to calm herself, "Okay…"  
  


Rouge then asks Eggman her question, "Have you found out what is wrong yet?"  
  


Eggman grunts then begins to answer Rouge's question as he continues to work, "I'm checking the Ark's systems while doing a scan of the inside of the Ark, if anything is out of order either I or Tails will find it…" as he finishes Eggman's face turns quite pale and his mustache quickly droops down below his chin.  
  


Rouge quickly asks him, "What's wrong? Did you find out what's going on?"  
  


As Eggman loads his findings to Tails he begins to speak to Rouge, even as Tails' face, covered with fur pales to the same shade, his tails lying on the floor motionless, "According to this, there is a wave of unknown energy traveling through the Ark, gaining speed exponentially, it will soon engulf the entire space colony and us with it."  
  


Knuckles quickly speaks up, "Whoa, wait a minute, where did this 'wave' come from?"  
  


Tails, after reading the data, answers Knuckles in a flat voice, "It looks like that when the eclipse cannon didn't fire, the chaos energy stored in it did not dissipate even after we had stopped the chaos emeralds, when Shadow and Sonic used chaos control on the colony it must of caused a chain reaction, releasing the stored chaos energy."  
  


Sonic quietly gets up, "How long until the wave gets to us?"  
  


Both Eggman and Tails turn towards Sonic with the same look of doom on there faces, "It's already here"  
  


As they say that Amy begins to scream, Sonic turns just in time to see a wall of white light hit him full in the face.  
  
  


**Outside the Space ****Colony**** **Ark******:  
  
**

_From outside the colony, it appears to fill with a strange pure white glow.  
The glow quickly grows stronger until the colony can no longer be seen through its intense glare.  
As the white glow, now light, reaches its peak, it suddenly disappears, blinding any observers with the sudden darkness._

_The Space __Colony__ _Ark___ is gone…  
  
_

**_DISCONTINUITY  
  
_**

**Year: 20XX  
  
NEO TERRA:**

**Population: Over 7.0 Billion Sentients**

**Climate: Controlled  
  
**

**Largest Military/Law Enforcing Group: the Global United Nations or G.U.N.  
  
**

**Main Base of Operations: ****Station Square******

**Official  
Divisions of G.U.N.: The Global Navy Armada (GNA)  
                                  The Global Armed Forces (GAF)  
                                  The Advanced Rescue Command (ARC)  
                                  The Global Aeronautics Administration (GAA)  
                                  The Global Police and Law Enforcement Agency (GPLEA) (Nickname: Global Police)   
  
Heads of Divisions:  Admiral Davis Mackenzie (GNA)  
                                  General Li Wong (GAF)  
                                  Prof. Ivo Robotnik (in the stead of Founder Prof. Gerald Robotnik) (ARC)  
                                  General Mikala Novenko (GAA)  
                                  Supreme Chief Louis Stein (GPLEA)  
  
Currently Most Wanted by G.U.N.:**

**                                  Ambrosia:       _Leader of the worlds most powerful environmentalist group  
                                                          Charged with various counts of Eco-Terrorism, Sabotage,_**

**_                                                          Murder, Blackmail, Kidnapping, Destruction of Public and  
                                                          Private Properties, Etc.  
                                  _**

******Miles Prower: _A _Highly Intelligent Robotics Expert and Incredibly Young.  
                                                          Charged with various counts of Murder, Theft, Destruction of  
                                                          Public and Private Properties, Illegal Military Actions, Kidnapping,  
                                                          Smuggling, Attempted Assassinations of various Political figures,__**

**_                                                          Manslaughter, Etc.  
  
_**

******Mr. X (Real Name unknown): _A Thief that has been able to steal all Items that he wishes to steal  
                                                                                      Charged with Theft (all forms), Number of offences over 2000._**

****

****

**SPACE ABOVE NEO TERRA:  
  
**

As the light died down Sonic and the others quickly noticed that they were fine, the space colony appeared in the same place, had any of them checked the moon, they would have quickly realized that something was definitely wrong.

**NEO TERRAN SURFACE (****STATION SQUARE****: RESIDENTIAL DISTRICT):  
  
**

Cream sat in her room watching the stars, her friend Cheese sitting beside her, the small Chao cooing as she spoke to him about her wishes and dreams, "Someday Cheese, I wish people would stop fighting over things and work together to solve there problems, what would you wish Cheese."  
  


The Chao cooed as it thought about its answer, but as it did a sudden burst of bright light filled the sky, Cream turned quickly to the sky, "Wow, it's beautiful, do you know what it is Cheese?"  
  


The Chao just shook it's head no as the light quickly died down and the sky seemed to return to what it should have been, a knock then came from Cream's bedroom door as her mothers voice came from the other side, "Cream, open the door, it's your mother."  
  


As Cream opened the door her mother quickly saw Cheese still sitting by the window, "Cream how many times do I have to tell you, pets stay outside, that's why we build that house for him in the yard."  
  


Cream turned to her mother and calmly protested, "But mom, Cheese is my friend, and you don't leave friends in the cold when you have somewhere warm  to go and spend the night."  
  


Cream's mother shook her head, "Cream I'm not going to start that again with you right now, besides I just came to make sure your all-right." She bent down and hugged Cream, then picked her up and put her in her bed.  
  


"Now go to sleep Cream." Said Cream's mother as she closed the door after taking Cheese with her.  
  


Cream waited for the sound of the back yard door sliding open, then shut before carefully getting out of her bed and slowly opening her window.

She checked for her mother before calling Cheese, "Cheese, it's alright to come back now, she's gone."  
  


The Chao walked out of its small house in the backyard then carefully flew up to Cream's window with a happy Coo.  
  


None noticed the strange figure in the tree behind the house.  
  


**The Tree:**  
  


Prower watched the little girl Cream as she once more let her pet Chao into her room, her actions reminding him of the few good memories he had.  
  


He once more turned his attention to the one he really had come to watch, He wondered what the young girl Cream had deserved to have a mother like the woman he was watching.  
  


That woman had been apart of that group that forever ruined his life, his childhood, he never had a chance…  
  


_FLASHBACK:  
  
_

_"HEY, **Two tails, where you going, you haven't gotten you daily pounding yet."  
  
**_

_Scared for his life Prower ran for his life, he continued to run as he entered a part of the orphanage that he had never had been before.  
  
_

_As he chanced to look behind him he ran right into Cream's Mother, then she had been a worker at the orphanage where he lived, she looked down at him, "What are you doing here? This is a restricted section, you shouldn't be here, you're in big trouble, and what did I tell you about waving those two things around?"  
  
_

_As she continued ranting he realize he had forgotten to hold his tails together, everyone in the orphanage hated him, hated his tails, he hated his tails, because of them everyone called him a freak, because of them he lost his parents.  
  
_

_Prower heard footsteps approaching, ***I don't have time for this*, Prower muttered a soft "Sorry" then quickly ran past Cream's mother.  
  
**_

_Cream's mother screamed at Prower as he ran past, "Hey, what are you doing, come back you freak!"  
  
_

_That was the last thing he heard as he rounded the corner, as he ran down this new corridor he tripped and fell into an old side table in the hall, a rusted old oil lamp fell to the floor, this would of not mattered had that wing not been under renovation, a hot light that had been left on ignited the oil and began the fire.  
  
_

_END FLASHBACK  
  
_

Prower closed his eyes vainly to hide from the memories flooding through his mind, one of his hands absently reached up to the metal mask that covered the burned remains of his face. The specialized optics he had placed in the masks eye sockets focused silently as he looked once more towards Cream's mother, their burning blue light thankfully hidden by the tree's leaves.   
  


As he prepared the focused cutting laser he had grafted to the cybernetics in his arm, he could taste his revenge and picture the woman's mind boiling away in an instant as the laser pierced her skull, a bright flash lit the sky, he, Cream, and practically everyone else that night turned and watched the light as it filled the sky.  
  


While everyone else continued to watch he quickly leapt from the tree and ran, he didn't know what that light was but he didn't need it to expose him to his target.   
  


As he ran he quickly let his thoughts go to the light in the sky, he wondered what it could be, what caused it, _*where is that light coming from?*_, but just as quickly the light disappeared.

He slowed when the light disappeared, he quickly turned his mind back to escape when he rounded a corner and spotted his vehicle, a black and blue machine of his own creation.  
  


As he quietly closed the canopy he wondered what that light had been, what he did not know was that no-one on Neo Terra knew what it was, or what adventure it brought with it.  
  


**END CHAPTER ONE OF ALTERATIONS  
  
**


	2. ReEntry

**SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
  
**Re-Entry…****

**INSIDE THE SPACE COLONY:  
  
**

"Is everybody alright?" asked Sonic as the others as his head cleared.  
  


Everyone nodded or said they were alright, Knuckles looked around then asked, "Does anybody know what just happened?"  
  


Tails quickly answered, "I don't know, I'll check to see if the Ark's sensors recorded anything on that wave."  
  


Eggman, after pinching himself to see if he wasn't dreaming (while no one was looking), made an announcement, "While Tails is doing that I'll check the Ark's structural integrity, we should make sure that whatever that wave was didn't damage the Ark in a way that may lead to a hull breach."  
  


Just as he reached the console the Ark made an all too familiar sickening rumble, as she braced herself against the wall Amy cried out, "What's going on? I thought Sonic and Shadow had stopped the Ark from falling anymore."  
  


As the shaking subsided, Tails answered Amy's question, "The wave scrambled the computers that control the Ark's orbit. The computers are causing the Ark's orbital rockets to misfire, they've pushed us back out of orbit."  
  


Quickly typed something into the console, "There may be a way for us to get out of here, there are some un-used escape pods in the lower decks of the Space Colony, if we can reach them then we can escape the Colony before it re-enters the Earth's atmosphere!"  
  


Sonic started towards the door, "Then what are we waiting for, lets move it."  
  


Rouge followed as Sonic left, "No arguments here."  
  


Eggman then turned to Tails, "You better get that walker of yours ready, we'll need it's and the Egg Walker's firepower to break some low level security doors on the way." While Tails wasn't looking, Eggman quietly opened Tails' briefcase a grabbed one of the Chaos Emeralds, then quietly closed it again before getting into his Egg Walker.  
  


Knuckles turned to Shadow as Tails and Eggman left in their Walkers, "Well, aren't you coming, or are you going to stay here?"  
  


Shadow looked at Knuckles, some exhaustion still in his eyes,  "I was just thinking about something, come on, you don't want to get left behind do you."  
  


As Shadow and Knuckles raced out the door, Amy quickly followed, "Hey, don't you guys dare leave me behind!" *_Why do they always leave me behind?*  
  
_

**SPACE COLONY CORRIDOR (10 Minutes to Impact (again)):  
  
**

_Alarms blare throughout the colony, automated security doors close and computers containing secret information shut down, only to be activated again by numerous codes.  
On one of the lower levels, a window begins to loosen as the Ark once again enters the atmosphere, even thought it's decent has been slowed by the now working computers meant to control the Ark's orbit now attempting to put the Ark back into orbit. A few meters down the corridor, a security door rattles, then bursts forward as it is blown open by the Egg Walker and Tornado 3 _(AN: It is the Tornado 3 you can see the 3 only if you look closely though.)_._  
  


Amy looked down the darkened corridor, "Where are we, are you sure you know where we are going?"

Eggman looked down to Amy from the Egg Walker, "I've used the Egg Walker's own computer to access the Ark's systems, Ms. Rose, the escape pods are just ahead."  
  


Tails then maneuvered the Tornado 3 towards a nearby window, "It look's like something's slowing the Ark's decent, it looks like we're already in the Earth's atmosphere."  
  


Rouge turned towards Tails, "What do you mean…  Look Out!"  
  


The window beside Tails was shaking and beginning to crack because of the vibration, it quickly shattered pulling Tails, Sonic, Knuckles, and Amy out of the Colony.

Shadow quickly grabbed Rouge and a near by support before she too was sucked out, Eggman quickly typed on his console in the Egg Walker as it too began to be pulled out.  
  


Emergency shutters quickly closed over the window, as they did Shadow let go of the support, Rouge turned to the others, "They're gone…"  
  


Shadow looked down as Eggman shook his head, "I may have wanted to kill that hedgehog, but not even I wanted it to happen like this."  
  


A large rumble and groan echoed throughout the Colony, "Hurry, that breach probably has weakened the rest of the Colony's hull integrity, even if the Colony's decent has slowed we must still evacuate."  
  


With that the trio began to continue down the Colonies corridor, to the escape pods, and their new world.  
  


**SOMEWHERE IN THE ATMOSPHERE OVER ****STATION SQUARE****:  
  
**

It was cold, very cold, as Tails struggled to stay conscious and change the Tornado into flight mode.  
  


Amy was falling nearby, unconscious, Sonic holding her while holding onto the Tornado to keep both from tumbling away, while Knuckles held onto the other side of the Tornado.  
  


As the wings finally fully extended, Tails began to try to slow their decent, he put the Tornado's jet engine in full reverse, turning while pointing the nose up to lose speed.  
  


The air began to warm as they dropped lower into the atmosphere, Sonic, still holding Amy looked to Tails wearily, "I own little buddy."  
  


Tails just shook his head no, just then Knuckles spotted something familiar, "Hey, isn't that the Mystic Ruins train station?"  
  


Sonic looked ahead, "Hey, yeah it is, hey Tails, why don't you make another pass and lets park this thing in your workshop."  
  


Tails smiled and saluted Sonic, "I'm on it Sonic."  
  


**SOMEWHERE OUTSIDE OF ****STATION SQUARE**** (a few minutes after the above):  
  
**

Eggman, Rouge, and Shadow, carefully exited their escape pods, which had landed on some cliffs outside of Station Square.  
  


On a whim Rouge looked up into the sky, as if to look for the fallen heroes, and noticed the moon, all thoughts of the others left her mind, "Hey boys, this may sound strange, but has anybody looked at the moon recently?"  
  


Shadow and Eggman looked at Rouge strangely, Shadow then blinked a couple times then looked up into the sky, Eggman on the other hand wasn't as calm, "What are you talking about Rouge, what do you mean look at the…" He stopped when he did look up and noticed the moon, "…IMPOSSIBLE!!!"  
  


Shadow stared at the FULL moon, "If I'm not mistaken we destroyed have of that moon, so what happened to that damage?"  
  


"Or us…"   
  


Shadow and Rouge turned to Eggman, "What are you talking about?" Rouge asked.  
  


Eggman turned back from the moon towards Shadow and Rouge, "I've been thinking about that energy wave that passed through the Ark, since it was caused by Chaos energy then it is possible, just possible, that that wave was a form of Chaos Control." A smile appearing on his face as he finished.  
  


Rouge's jaw dropped, "Chaos Control? Are you saying that this isn't Earth?"  
  


Eggman smile just got larger, "Maybe not our Earth."   
  


The implications of Eggman's words, quickly dawns on Rouge, "Which means that no-one knows what happened, and maybe no-one knows us…"  
  


Shadow also smiled,_ *and I still keep my promise to you Maria, even if I still work for the 'good' doctor*_.  
  


**MYSTIC RUINS (Old Airfield):  
  
**

Tails brought the Tornado round for another pass, as he did Tails pressed the toggle to ready the runway, then he frowned.  
  


Sonic quickly noticed his friend's expression, "What's wrong Tails?"  
  


Tails quickly turned to Sonic then back to the darkened runway, "Something's wrong, I just turned on the runway lights but the runway is still dark, I had just finished testing them before I found out that you had been arrested."  
  


Sonic looked down at the darkened runway, "Are you sure they didn't burn out or something?"  
  


Knuckles turned to look at Tails, "What are you two talking about?"  
  


Tails just shook his head, "It's nothing, everybody hang on tight, we're going in."  
  


**FIVE MINUTES LATER:  
  
**

Sonic shook his head as he walked towards the door of the old air terminal, "Tails, I can't believe you still have trouble landing that thing, you have got to… … Tails what happened to your workshop?"  
  


On Earth the old air terminal had been converted into Tails' workshop, but on Neo-Terra…  
  


Amy, who had been woken by the 'landing', walked up beside Sonic, "Tails, this place is a dump, don't you ever clean it up?"  
  


When Tails walked into the terminal, he was dumbfounded, where he expected his various machines and unfinished projects he found old avionics equipment, dust, webs, and a lot junk he was sure that he had thrown out when he first got the place.  
  


Tails' jaw dropped, he grunted a little in surprise before he could himself together, "I don't know, half this stuff I'm sure I threw out when I first got to use this place as my Workshop."  
  


Knuckles, who had walked in after Amy quietly walked over to a counter and wiped his finger along the top, "This place looks like it hasn't been used in 50 years."  
  


(AN: Why is it always a multiple of 5 or even number of years in these things (Games, movies, etc.))  
  


Sonic just shrugged, "Well whatever happened here, why don't we help Tails get this place back together, besides, we owe him."  
  


Amy smiled, "Yeah, hey Knuckles you going to help to?"  
  


Knuckles shrugged, "I might as well, since I have the Master emerald with me I don't have to worry about it being stolen when I'm gone, and I have nothing else to do."  
  


Tails was touched by his friends' kindness, "You guys really want to help me get this place back together again?"  
  


Sonic put his hand on his friend's shoulder, "Of course we do, were friends, and besides, like I said, we owe you."  
  


Tails smiled as he and his friends began to clean up the old terminal.  
  


**ADVANCED RESCUE COMMAND HEADQUARTERS (Robotics Lab):  
  
**

Shadow walked into Robotics Lab, and once more found Robotnik working on one of his "Inventions".  
  


Shadow smiled as he spoke, "Professor Robotnik," he paused as Ivo instinctively sat up at his name being called, unfortunately for him he had his newest project above him when he did so.  
  


Clunk!  
  


Shadow then continued, "You need to report to the main briefing room, Gun is calling in the heads every department for this, whatever it is."  
  


The Professor got up and rubbed his head a bit before he answered, "Do you have to keep doing that?"  
  


Shadow smiled, "Doing what? Besides, you have to get to that briefing room."  
  


As they left that room, Ivo turned his head to Shadow, "Do you think this is really that important?"  
  


Shadow just looked to Ivo, "You spend way to much time in that room, you should at least put window in there or something, then maybe you would have seen it."  
  


Ivo looked at Shadow seriously, "Seen what?"  
  


Shadow shook his head, "About half an hour ago, there was a massive disturbance in orbit around Neo-Terra, whatever it was lit up half the planet before it stopped, for crying out loud it lit up the Cafeteria from the Lobby!"  
  


Ivo was shocked, especially since there was about 100 feet and 5 corners between the Lobby and the Cafeteria, "What?!"  
  


Shadow continued further, "That's not all, when it disappeared we detected a large mass in its place, our scans were able to confirm that whatever it was, it was built along the lines of a Bernoulli spherical space colony, but for some reason began to lose orbit and quickly entered the atmosphere, other than that I have nothing to tell you."  
  


As they came to the Briefing Room Ivo turned to Shadow, "Let's hope they tell me what's going on."  
  


**END CHAPTER TWO OF ALTERATIONS  
  
**

**  
**  
  



	3. and a New Adventure

**SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
  
**… and a New Story.  
****  
  
****

**ADVANCED RESCUE COMMAND HEADQUARTERS (Briefing Room):  
  
**

Robotnik and Shadow quickly sat down at the large round table in the Briefing room, Robotnik sitting in the slightly larger of the chairs, he then quickly typed something in on a keypad on one arm of the chair.  
  


A light came on in the middle of the table, and from that light six holographic faces appeared, one of which surprised Ivo more than Shadow had earlier.  
  


"Madame President, I didn't expect you to be in on this."  
  


The President put on a wry smile, "I can see that Professor, you still have some oil on your head."  
  


Shadow snickered as Ivo quickly tried to wipe the oil off of his head, one of the other faces cleared his throat, "Um, Madame President, I believe we should get back to the subject at hand."  
  


The President just nodded her head, "Quite right, Mr. Stein, let's get to it then, General Novenko, what is the situation?"  
  


As Novenko began to speak an image of Neo-Terra appeared above the faces, "As you most likely know, at 19:00 hours a large disturbance was picked up in orbit around Neo-Terra, which was soon replaced by a large mass, appearing to be a Spherical Bernoulli Space Colony, this mass then entered the atmosphere, crashing into the ocean off the coast near Station Square, Admiral Mackenzie."  
  


The image of Neo-Terra shifted, zooming in on the Ocean, "When the mass impacted the ocean, I immediately sent a survey team to investigate the area, it should be arriving now, if you wish Madame President, I could patch us into them now."  
  


The President nodded her head, "Patch us in Admiral."  
  


The image changed again, this time to a visual of the sea floor, "Captain Luca, this is Admiral Mackenzie, how long until you reach the mass?"  
  


"Not long now sir, I should be near enough to the mass to get a visual soon…    (Stuttering sounds)    …I DON'T BELIEVE IT, LOOK AT THE SIZE OF THAT THING!"  
  
The Image showed the Space Colony Ark, some of the outer hull had been burned or buckled by re-entry but most of the Colony remained intact, as the visual began to pan around to the front of the Colony the President and Heads of G.U.N. gasped.  
  


Ivo, Shadow, and The President, all paled, Shadow was the first to speak, "It can't be."  
  


The grim faces of the others only confirmed what they saw, Ivo shook his head, "An Eclipse Cannon."  
  


The President put on a stern face, "This is a serious matter gentlemen, I want all of you to contact me again tomorrow at 16 hundred hours, Professor Robotnik, Shadow, I'd like to speak with you privately."  
  


As the other faces disappeared the President looked seriously at Ivo and Shadow, "Ivo this is serious, only Grandfather knew how to make an Eclipse Cannon, I need you to go through his dairy to see if he left any information on a second Cannon, hurry I don't think we want to waste any time."  
  


Ivo quickly got up and left the briefing room, Shadow stayed behind, "Is there anything you want me to do Maria?"  
  


President Maria Robotnik shook her head, "I don't think there is anything you can do about this right now Shadow, except maybe to stop surprising my cousin."  
  


Shadow smirked, "What makes you think that?"  
  


Maria smiled one of her truly happy smiles, "I recognize that smudge on his forehead anywhere, I made him make that same smudge on too many of his early experiments to count Shadow, I know exactly what you did."  
  


Shadow smiled, "Right Maria, I'll stop, for a while anyways, but he spends too much time working on his projects in that room anyways, this time he won't even let me see it, he keeps it in this box that only he can open."  
  


Maria just nodded, "I know, and it's alright to get him out of that room Shadow, but he loves working on his machines too much for him to just stop, even if he is head of A.R.C."  
  


Shadow turned and began to leave the room, "I hope to see you again soon Maria."  
  


Maria sighed, "You to Shadow, goodbye."  
  


Shadow began to close the door, "goodbye, Maria."  
  


When the door closed, Maria's face disappeared, the image of the Ark still projected above the round table, unfortunately they forgot to tell Captain Luca to close the channel, "Hello, anybody still there, Hello?"  
  


**G.P.L.E.A Branch, ****Station Square****:  
  
**

Rouge gave a small sigh as she removed her body armor, "I can't believe one flash of light can cause THAT much trouble."  
  


The rookie, a young human, to her right laughed, "I know what you mean, in fact I'm surprised that Ambrosia or her Eco-gang didn't use the chaos to make another one of their attacks."  
  


Rouge smirked, "It's not really Ambrosia that you have to really worry about, for being a terrorist she's pretty predictable, no, it was Mr. X that I was worried about."  
  


The rookie was shocked, "I thought that guy was media-hype, you mean he's actually real?!"  
  


A more experienced rookie, a puffin, turned to the other, "You bet he is, and Rouge here almost caught him once, didn't you?"  
  


A thoughtful look crossed Rouge's face, "Yeah, I almost had him, it was the last time the Echidna's had lent the museum one of their sacred jewels for research, the chief thought it best to have experienced officers on hand in case that someone tried to steal it, when the silent alarm went off a ran for the exhibit and arrived as he was climbing up to the window, I took off and beat him to the window, but as soon as he saw me he tossed the jewel towards the floor, I dove for it and he got away."  
  


The human rookie blinked with surprise, "That would mean you actually saw him, you must be the only person on the planet to actually see him!"  
  


As Rouge finished getting back into her street clothes she smiled, "Yeah, I guess I am, well I got a cab to catch, later girls."  
  


Rouge then left the change room and headed out to the street, and tried to hail a cab, after about three drove by she gave up, _*I guess I'm not getting a ride tonight, oh well, a flight would do me good*._  
  


She took a quick look around, then above, then spread her wings and took off into the night sky for home.  
  


**END CHAPTER THREE OF ALTERATIONS  
  
**


	4. Back to Normal?

** SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
  
**Back to Normal?******  
  
******

**Abandoned Power Plant (Eggman's New Base):  
  
**

Rouge turned to the others, "This is your new base? The place looks ready to fall down on us any minute."  
  


Shadow continued to look around at the decaying turbines, "I certainly don't see why we're here, or why that man gave you the deed to this place in the first place."  
  


Eggman's face developed a sour look, he took a deep breath before breathing, "Have either of you ever wondered how I am able to get resources for my plans so easily?"  
  


Rouge looked around again before answering, "Not really, but I'm sure your going to tell us."  
  


A wry grin crosses Eggman's face, "This plant was once powered by coal furnaces, coal is pure carbon, and so are Diamonds."  
  


Rouge turned to Eggman faster than normal, "You mean you MAKE DIAMONDS?!?!"  
  


**Mystic Ruins (Old Airfield):  
  
**

Amy picked up a part of an old ham radio from the floor, "Hey Tails, what do you want to do with this thing?"  
  


Tails looked up from the Tornado 3, which he had pulled in once some space had been cleared, and pointed over to a small pile of electronics "Put over there Amy, I might be able to do something with it."  
  


As Amy put the part into the pile indicated Knuckles set down a box of old things, "Hey Tails, why aren't you throwing out this stuff, most of it's junk anyways."  
  


Tails picked up the box and put it in the back of the Tornado, "I know, but somebody might want it, even if it is just for the metal."  
  


Sonic came down from upstairs, "The rooms upstairs weren't too bad, if you don't mind dust, and the antique look."  
  


Tails pushed open the doors to the landing strip, "I'm going into Station Square to get rid of this stuff and pick up a few things, you guys could stay here if you want, it's been a while since anyone's slept."  
  


Amy turned to Tails, "Are you sure?"  
  


Tails nodded, "It's fine, go on, I'll be back in awhile."  
  


With that he got in the Tornado and headed off for Station Square.  
  


**Station Square (Residential District):  
  
**

Cream yawned as she walked down the street, Cheese sleeping on her shoulder peacefully as they headed for the shopping district in the morning light.  
  


Her mother had sent her out to get some groceries and exercise so that she wouldn't sit in front of the TV all morning watching cartoons, not that Cream minded since her Saturday walks gave her a chance play around with Cheese.  
  


Cream finally reached the park where she and Cheese played, she gently woke the Chao sleeping on her shoulder, "Cheese, wake up Cheese where here."  
  


The Chao woke up and cooed as it took off of Cream's shoulder, then Cream began to run after Cheese, as she did she began to flap her ears, Cream took off.  
  


**Outside of Station Square:  
  
**

Tails walked into Station Square carrying the box after parking the Tornado outside of the city, even if the police weren't after him for rescuing Sonic anymore he would rather not have to much attention, and a vehicle like the Tornado isn't that common.  
  


After he had walked for a while an accented voice cried out, "Excuse me, you, over there, could I speak with you for a moment?"  
  


Tails turned to the voice, it came from a thin man who was stepping out of the nearby building, the man puffed slightly as he finished rushing across the street, "Thank you for stopping, I almost thought that you were just going to keep walking. Um may I ask what you intend to do with the items in that box your carrying?"  
  


Tails looked at the box then back to the man, "This stuff, well I was thinking about whether or not I could find someone who would want this stuff since most of it still seems pretty good and it'd be a waste to just throw it out."  
  


The man looked very relieved, "It's a good thing I saw you then, you see I work for the Station Square museum and was to prepare an exhibit on recent history from the past hundred years, but I found that the their were no pieces for the exhibit, if your willing I'll take those items for you."  
  


Tails smiled as he answered, "Really? It's alright with me, here, I'm just glad I don't have to throw it out."  
  


With that Tails gave the man the box, as Tails began to leave the man stopped him, "Oh, before you go young man take this, I feel I need to give you something for your troubles."  
  


The man then pushed some money into Tails' hand, "You don't…"  
  


The man shook his head, "Keep it, as a reward young man, by the way my name is Arthur, may I ask yours?", he asked as he extended his hand.  
  


Tails took Arthur's hand and shook it, "I'm Tails."  
  


Arthur looked at Tails confused, "Tails?" That was when Arthur noticed Tails' unique appendage, "Oh, I see, well thank you for your help Tails, I hope we meet again some day."  
  


Tails nodded, "I'd like that, well goodbye."  
  


Arthur began to turn towards the building he had come from, "Goodbye."  
  


With money in hand Tails continued to walk.  
  


**Station Square (Shopping District):  
  
**

Cream finished paying the cashier for the groceries, "Thank you very much."  
  


Carefully Cream picked up the bag of groceries, once she left the store she turned and walked to the side of the store, there she waited, "Alright Cheese, it's safe to come out now." She spoke as Cheese came out of hiding and landed on her shoulder.  
  


As Cream turned to head home she accidentally walked straight into Tails who had just left the store.  
  


Cream quickly got up and began to pick up her spilt groceries, "I'm sorry for running into you, I should have been more carefully."  
  


Tails began to pick up the groceries he had also spilt, "No, It's alright, I should have been looking where I was going."  
  


As they picked up their groceries both tried to pick up the same thing, their hands touched, with that they both looked up at who they had run into, and blushed.  
  


**END CHAPTER FOUR OF ALTERATIONS**  
  



	5. Preparations and Investigations

**SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
  
**Preparations and Investigations.  
  
********

**G.N.A. Vessel (en route to Space Colony Ark):  
  
**

Maria and Shadow stood on the bow of the G.N.A.'s most advanced naval research vessel as it sped towards the submerged space colony, worry and sea spray the only things showing on their faces.  
  


Ivo came up from behind them, shaking his head in confusion, "I checked 12 times, there is nothing in grandfather's diaries about a second Eclipse Cannon, I even checked for hidden messages, codes, everything and the only thing that was legible looked like a shopping list."  
  


Shadow turned around to look at Ivo, "A shopping list?"  
  


Maria sighed, "You tried your best Ivo, (sigh) anyway, we'll be arriving at the site in a few minutes, you better go get ready for the dive."  
  


Ivo nodded, "Your right Maria, I guess this whole thing is starting to get to me, maybe I'll work on my project for a bit."  
  


As Ivo left Shadow turned to Maria, "You haven't said much while we were out here Maria, I'm starting to wonder if all of this is starting to get to you."  
  


Maria looked back to Shadow and forced a small smile, she nodded, "It is getting to me isn't it, but there is nothing funny about an Eclipse Cannon, we both know that Shadow, we have to find out where this one came from, otherwise the world may be in great danger."  
  


Shadow nodded, then both turned back out to look at the sea.  
  


**Abandoned Power Plant:  
  
**

Shadow checked a clock Eggman had hung on a wall as he walked by, "It's been half an hour and she just calmed down?"  
  


As Rouge finally came to her senses she turned on Eggman, "If you could make diamonds all this time why didn't you just buy the planet?"  
  


Eggman turned his back to Rouge and got back to his work, "If I started just using diamonds for everything how long do you think it would take before those same diamonds become worthless Rouge? Besides I'm only going to use these to get some items I can't build here with what I brought with me from my old base."  
  


Rouge thought about it then nodded her head, "Yeah, I guess your right…"  
  


Eggman then grabbed something out of his pocket then turned to Rouge as she was about to leave, "Oh, Rouge, you think you could do something for me?"  
  


Rouge turned around and faced Eggman, "Like what?"  
  


Eggman grinned, "A little reconnaissance mission, that's all."  
  


Rouge tilted her head, "Alright, so just what is that you want me to do?"  
  


Eggman tossed her the small device he had taken from his pocket, "Attach that to a data port or open phone line somewhere in the city, then see how the natives and the government are reacting from our little arrival."  
  


Rouge looked at the thing in her hand, "Fine with me, and just what are you going to be doing while on this mission of yours?"  
  


Eggman snickered as he turned around, "Why Rouge, it wouldn't do to give away everything now would it?"  
  


With that Eggman began to laugh manically while he started to work on his next project.  
  


**Space Colony Ark (Submerged (Airlock)):  
  
**

The space colony was cold and dark under the water, most of its systems had shutdown or been damaged on re-entry and the sound of water drops could be heard echoing throughout the colony's corridors.   
  


There was a clang as Maria, Ivo, Shadow, and team of G.U.N. personnel docked there submersible with the abandoned colony, and a hiss as the airlock opened allowing them inside.  
  


Ivo stopped holding his breath when he realized the pressure of the submersible and colony were the same, "Something must be running if this thing's pressurized itself."  
  


Shadow tried not to laugh at Ivo who was just returning to a normal skin colour as he spoke, Maria walked over to one of the nearby walls, "It feels like I'm back in grandfather's lab again, like he's going to turn on the lights of the corridor and ask why I'm up so late like he did when I couldn't get to sleep"  
  


Shadow came up beside Maria and put his hand to the wall, "It is like his lab, isn't it?"  
  


Ivo began to walk down the corridor, "If it is like grandfather's lab then… Ah ha, here it is!"  
  


With Ivo's shout the lights in the colony turned back on, Maria, Shadow and the others quickly moved to join Ivo.  
  


Maria was the first to figure out what her cousin found, "A system terminal!"  
  


Ivo began typing on the terminal, "The main computer is under lock-down but I found another active terminal that has access, according to this map I pulled up it's here, down the corridor on the left, we should also probably try to secure the Eclipse Cannon's control room, here."  
  


Maria turned to the others, "Ivo, Shadow and I will find the terminal, the rest of you should secure the control room."  
  


When the others left Maria, Shadow and Ivo quickly found the terminal.  
  


**Station Square:  
  
**

Rouge watched as people continued to walk by her, she had heard a lot of people talking about the light they saw in the night sky, none of them having any Idea what it really was.  
  


Rouge chuckled to herself as she got off the bench she had been sitting on, thinking how easy it was she almost missed the paper that someone had left on the bench before her, she picked it up then almost choked, "Eggman's going to have a heart attack when he sees this!"  
  


With that see began to make her way back to the base.  
  


**Space Colony Ark (Abandoned Lab):**

Ivo quickly began to try to access the main computer, "No wonder I couldn't get in from the wall terminal, half of the main computer's resources are stuck in a frozen program, the other half in diagnostics, I won't be able to much of anything from here until they run there course."  
  


Just then Shadow spotted something on the floor, "Ivo, isn't that your grandfather's diary over there?"  
  


There, on the floor, rested the diary disc of Prof. Gerald Robotnik.


	6. But through a glass darkly

**SONIC ADVENTURE 2: ALTERATIONS  
  
**

**DISCLAIMER: **Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
(The same goes for the guys who I got this title from)  
**READ THIS **à(WARNING: Part of the Chapter may need a higher rating!)  
**"But through a glass darkly…"  
  
**

**Abandoned Power Plant:**  
  


Rouge quickly ran in as the doors slammed shut behind her, "Wait till you guys get a look at this!"  
  


Shadow calmly turned towards Rouge while Eggman looked up from the robot he was working on, Shadow walked over to Rouge, "What is it?"  
  


Eggman came over and looked over Rouge's shoulder, "So, what have you got here for us Rouge?"  
  


Rouge opened up the paper to the first page and lifted it so the Shadow and Eggman could see, "Recognize somebody?"  
  


Shadow and Eggman stepped back in surprise, "I don't believe it!"  
  


**Space Colony Ark (Abandoned Lab):  
  
**

Ivo bent down carefully and picked up the disc on the ground, "What? You're right, it really looks like my grandfather's diary, but what would it be doing here, huh?"  
  


Shadow stepped forward, "What is it?"  
  


Ivo looked towards the console, "The disc seems different for some reason, Shadow. I'm going to see if I can use the console to read the disc."

Shadow looked at Ivo, "Are you sure this is the time to review old memories Ivo?"  
  


Ivo carefully put the disk into the console, "If I'm right Shadow, this disc may help us figure out what's happening here…"  
  


**Old Airfield:  
  
**

Sonic yawned as he sat up in an old bed that had been left upstairs in the old air terminal, *_I just don't get why this place looks like Tails didn't live here, I guess it's a good thing that someone used to though. I wonder, maybe all this has something to do with that wave thing that hit us.*_ That's when Sonic's nose picked up on something coming from downstairs, "Hey, something smells pretty good".  
  


When Sonic got down stairs he found Amy using a small portable stove to cook something while Tails helped a rabbit he didn't recognize set up some plates and plastic silverware on a fold-up table, "Hey Tails, when did you get back?"  
  


Tails turned his head towards Sonic as he put down a plate, "Hi Sonic, I got back awhile ago, this is Cream, she's a new friend I bumped into at the grocery store."  
  


Sonic turned to Cream, "Nice to meet you Cream."  
  


Cream put the silverware she had on the table and curtsied, "It's a pleasure to meet you Mister Sonic"  
  
Sonic sweatdropped, _*Mister?!*  
  
_

**Abandoned Power Plant:  
  
**

There staring up at Shadow and Eggman from the front page of the paper was a picture with the caption _"Prof. Ivo Robotnik speaks at seminar on Advanced Robotics and Basic A.I."  
  
_Shadow looked up from the paper and looked at Rouge, "Is it just me or does the one in the picture look thinner?"  
  


Eggman grabbed at the paper, "Give me that."

Rouge snickered, "I'd say that's something important."  
  


Eggman began to flip through the paper, he stopped on about the second page, "Oh Rouge, you might want to look at this."  
  


Rouge came up and looked at the article Eggman was looking at, "Well, well, I didn't see that one."  
  


Shadow came up behind Rouge, "What is it?"  
  


The article was on Detective Rouge Bat.  
  


**Space Colony Ark (Abandoned Lab):  
  
**

Ivo was beyond all feeling, while Shadow wanted at that moment to do nothing more than find a quite corner and lose his lunch, breakfast and yesterday's supper.  
  


Shadow had been right about the disk being Ivo's grandfather's diary, and yet it wasn't.  
  


The entries in the diary never happened and when they exited the diary something came up onto the screen that they never expected, the last words of Eggman's Professor Gerald Robotnik.  
  


Just as Ivo ejected the disk and shut down the console, the Colony came back to life.  
  


Maria was just about ready to faint, she had been looking around the lab, wondering how on Neo-Terra it could be so much like her grandfather's when Ivo and Shadow found the disc, hearing that she was dead made her feel like someone was walking on her grave.  
  


The three were just standing there as the radio in Ivo's pocket came to life, "Ivo, Shadow, can any of you hear me?"  
  


Ivo shook his head then grabbed the radio, "This is Ivo, what is it?"  
  


"Sir, there's these things, there all over the place, we need help, Now! (_Gunshot's and Laser Fire) _Watch your back."  
  


They quickly came to their sense with that, Maria quickly turned to Shadow, "Shadow you should get down there and help them, Ivo, we'll head back to the sub, you need to find out what on Neo-Terra we just saw, I'm going to try to find a way to explain this to the department heads."  
  


**Ambrosia's Camp:  
  
**

Ambrosia was not a happy hedgehog, she rubbed her temples as she spoke "What do you mean 'I don't know what that light was boss.' I gave you the order to find out what that was and how it may affect our plans and all you come back with is 'I don't know'."  
  


The ferret cowered as Ambrosia got up and casually grabbed the handle of her hammer, "It's not my fault, the media doesn't have a clue and G.U.N. is keeping what they know so tightly under wraps that all my high clearance contacts know is that something is known, if they pried any further they'd be exposed and useless to us in the long run."  
  


As Ambrosia walked around the ferret she leaned in close to one ear, "You know, you're right, they would be useless if exposed (_She steps back_) but I can't let your failure go unpunished…"  
  


The ferret felt his leg break before he even realized what had happened, "…so consider that a warning, the next time you fail, it'll be your arm, then your chest, and if you survive that your head, got it?"  
  


The ferret nodded as he painfully remained standing, Ambrosia opened the tent's flap, "Get a medic in here for our friend's leg, I've got some private business to take care of."

The guard nodded and called for a medic as Ambrosia walked out into the camp. All the camp was, was number of tents and three plain huts, it was the smallest of the three huts that Ambrosia was headed for.  
  


Ambrosia motioned for the guards to step aside as she approached the hut, the shadowed figure inside looked up as she opened the door to the hut, "And how are you today brother dearest?"  
  


**END CHAPTER 6 OF ALTERATIONS**


	7. we see ourselves

**SONIC ADVENTURE 2: ALTERATIONS  
**

**DISCLAIMER: **Sonic and the Sonic Adventure series belongs Sega and Sonic Team,  
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.  
(The same goes for the guys who I got this title from)

"…**we see ourselves."  
**

**Abandoned Power Plant:  
**

Rouge read the article on her counterpart again while lounging on an old couch Eggman had brought in from somewhere,_So this is what I'd be like if I'd been a cop then, pretty boring if you ask me_, she smirked as she finished her thought.

Eggman had turned a small office into a personal lab and would leave every once in a while to get parts or something, every time he did Rouge went up to the office to see if she could get in and see what the old egg head was doing only to find the door locked and strange noises coming from inside.

After trying to peek through the window she went for her lock picks but decided against to picking the lock as she heard Eggman heading back, whatever was in there he didn't seem to want to leave it unsupervised.

It was about five minutes later that Eggman came back down to the main floor where they had been meeting with something under an old curtain he must of found somewhere, "Aaah, Rouge, Shadow, how would you like to see my latest project?"

Rouge put down the paper and walked over to the curtain, "It's about time you finished with it, whatever it is."

Shadow just turned his head towards it silently and continued to lean back against the wall.

Eggman smiled and swiftly pulled the curtain off of his project, "Behold, my latest invention!"

Standing there was something that looked like one of Eggman's E-1000 series (Mass produced, smaller versions of the E-100 series) except where it should have had guns it had two hands, both seemingly made up of a bunch of oddly shaped boxes, Rouge just looked at Eggman like he was losing the last of his few marbles, "Your going to take over the world with that!"

Even Shadow seemed mildly surprised, _I though it was a bomb._

Eggman just cleared his throat, "Not directly, this is my new construction bot, watch." Eggman opened quickly opened and closed a panel on the back of the bot and it came to life.

The bot looked around the room until it spotted some old spare parts and materials, then quickly walked over to the pile, some of the boxes in it's hands opened up to reveal tools or empty compartments as the bot began to construct something.

Rouge watched the bot work, "So, what's that supposed to be doing?"

Eggman smiled again, "Building the beginnings of my new army, first it will build another construction bot, then one of a selected group of my favourite robots before moving on to my true project!"

Rouge nodded her head, "Which you probably aren't going to tell us right now."

Eggman stood there gloating, "Actually I have something more important for us to do, while you two were sitting around I found us an opportunity too good to pass up."

Shadow got up off the wall, "Is that so, well then, you'll just have to tell us about this opportunity."

**Space Colony Ark:  
**

Shadow rushed down the halls of the abandoned colony towards the G.U.N. infantry, he could easily hear them from where he was, when he reached them he saw something strange.

The soldiers were being beaten, by water, inside the water Shadow could see strange devices floating near the tops, as he looked at the water creatures he saw one generate a tentacle, grab a soldier and throw him over Shadow's head.

Shadow turned back towards the lead of the creatures, "I've got to stop this."

Shadow charged the creature and jumped, the commander of the infantry turned to the others, "Give him cover fire!"

Shadow spun as he approached the creature's head, the thing noticed Shadow and retreated into itself, Shadow impacted the creature, and bounced right off, _What the?_

The creature turned to face Shadow, its head returned to its original place, its green sensor eyes glowed, then fired.

Shadow dodged the fire, and then jumped again, this time the creature had no time to retreat, the circuits of the devices in its head cracked and sizzled as Shadow sawed through them and their casings, the creature's head blew and the creature splashed to the floor, nothing but a puddle.

Shadow turned to the soldiers, "Aim for their heads!"

With that the soldiers fired and Shadow battled, all the while preparing to retreat to the sub.

**Ambrosia's Camp:  
**

The shadowed figure groaned slightly, then coughed a bit before speaking, "Leave me alone."

Ambrosia gave a laugh and began pacing around the hut, "If I had my way I'd leave you so alone you would never have to worry about anyone stumbling across you ever again, but, as you remember, mother and father made me promise to take care of you, too bad for you they never said how well or that I could never use you."

The figure looked down slightly, "It's not my fault they died."

Ambrosia leapt over to the figure, grabbed it by the shoulders and began to shake him, "NOT _YOUR_ FAULT! Do you really believe those words, they took you in out of pity, even though you are exactly what they were fighting against! A Freak! Nothing natural moves as fast as you, and yet you could do nothing to save them. The others told them that keeping you would bring trouble."

She pants then pauses as a thought calms her, "Though I guess I also have to thank you, without them dying I would of never been accepted into their pathetic passive resistance against those destroyers, them and their 'advanced technology' and 'progress' have done more damage to this world then we ever would of naturally, and you are probably a product of that."

The figure looked down, "What do you want?"

Ambrosia began to walk towards the door, "I want you to get ready, today is the day that they arrive in Station Square, and we will need you to be ready, you got that SONIC? Just remember what happened the last time you failed."

As Ambrosia left Sonic got up and moved into the light, his blue quills faded and broken, his face slightly sunken, and his eyes seemed to be focused far away, "I won't fail… … just as I won't forget."

**Old Airfield:  
**

Tails turned to Sonic again, "Hey, Sonic, how would you like to go into Station Square later?"

Sonic looked at Tails, "I don't know, why did you ask anyways?"

Tails continued to set the table, "I made another friend when I was getting rid of that stuff we collected, he works in the museum in Station Square, used the stuff to set up an exhibit."

Sonic scratched his chin, "Museum huh, come to think about it, I don't think I ever been there."

Amy called out from the stove, "That's because you've always been to busy running around to ever go there!"

Sonic scratched his head, "Oh yeah, heh heh."

Cream turned to Sonic, "Please Mr. Sonic, I've never been to a Museum before."

Sonic thought about it, "Sure…" his stomach grumbles "… but would it be alright to eat first?"

Everybody has a laugh then Sonic notices something, "Hey, where'd Knux go?"

**G.N.A. Vessel (Ocean Surface (Above Space Colony Ark)):  
**

Shadow helped one of the soldiers out of the sub as he and the others exited back onto the ship, "It's alright, just a few more steps."

The soldier turned to Shadow, "Thanks man, none of us could have made it without you."

Shadow shook his head, "Doesn't matter, besides, I was just doing my job, I'd never just leave somebody in a position like that."

An officer came quickly down the corridor as Ivo and Maria exited the sub, "Professor Robotnik, President Robotnik, there's a chopper waiting on deck for you and Shadow."

Ivo blinked, "Why is there chopper on deck for us?"

Then Maria brought her hand to her face, "The Ambassadors."

Ivo groaned, "The Echidna Ambassadors, with all this I'd completely forgotten about them!"

Maria nodded, "Thank whoever it was who remembered about the Ambassadors' arrival today and arranged for some faster transport."

Shadow came over to Maria and Ivo, after leaving the soldier with some medics, "So what are we meeting the Ambassadors about again?"

Maria began to walk down the corridor to the deck, "The Ambassadors are prepared to lend one of their sacred crystals to us again for study, the fact that they even contemplate this shows that they have confidence, in us, in G.U.N. and its divisions."

Shadow smirked, "This should be an interesting meeting then."

The three quickly reached the chopper and began their short flight to Station Square.

**Station Square (Outside Museum):  
**

The first thing out of Sonic's mouth when they got there was, "Whoa, what's going on here?"

In front of them was a huge crowd of people, press, and police officers, that's when Tails saw Arthur, he waved as he called "Arthur, hey Arthur, over here"

Arthur turned and looked around a bit before he found Tails in the growing crowd, he pushed his way over to the group, "Ah, Tails, for a moment I didn't think you'd be here, isn't it exciting?"

Amy came forward, "What's so exciting?"

Arthur looked at Amy like she had come from another planet, "You mean you don't know? The Echidna's are lending one of their sacred jewels, it's incredible, and especially considering that the last time they did the crystal was almost stolen."

Cream spoke up, "My mother told me about that, she said a man tried to take it for some reason."

Arthur looked down a Cream, "Very true, Ms…"

Cream looked up at Arthur, "Cream sir."

Arthur laughed, "Now, now, there isn't any need to be that formal, now quickly, come with me, these crowds would make it impossible for us to even get into the museum, but I still have access to one of the side doors since I work at the museum, we can look around at some of the exhibits until the Ambassadors come out with the jewel."

**Meanwhile Within the Museum:  
**

The Chief looked Rouge in the face, "Rouge this is important, more important than last time, your going to be in charge of the safety of the Ambassadors while they are in the museum, their bodyguards will be their as well, if something should occur you take your cues from them, you understand Rouge!"

Rouge nodded, "Yes Sir!"

The Chief looked thoughtfully, "Rouge, you understand that you're the best we've got, if I didn't think you were up for this you wouldn't be here."

Rouge smirked, "I understand, Sir, thanks for the complement, I just hope that I not going to be needed Chief."

The Chief smiled, "So do I Rouge, the Ambassadors will be here in five minutes Rouge, be ready."

With that the Chief left Rouge to wait for the Ambassadors.

**Outside the Museum Front:  
**

Ambrosia looked at the Museum carefully through the darkness from a nearby roof, "Few guards out front, but of course their going to use them to protect that jewel and the Ambassadors."

A grunt came up to Ambrosia, "Everybody's ready, should I order the attack?"

Ambrosia shook her head, "No, not yet, wait until the crowd dissipates or we have conformation that the jewels are in the open, if they even get the idea that we'll attack they bottle themselves up somewhere in that museum with the jewel and it would take too long to track it down."

The look at the crowd then started back for the group, "Got it."

Ambrosia smirked, "Everything's going according to plan."

**Outside the Museum Back:  
**

Eggman smiled as the reached the location, "Alright, here we are."

Rouge looked at the unimpressive back wall of the museum, "and here would be?"

Eggman began to pull a printout from his pocket, "This is the Station Square Museum, and we've come here to get this!"

As soon as Eggman opened the print out Shadow recognized the object on it, "A Chaos Emerald!"

Rouge smirked, "So that's your big surprise, well then, when do we acquire this Emerald?"

Eggman got into his Egg Walker, "Soon, the Emerald will be unveiled in a few minutes, and if we should need reinforcements, they are already on their way."

Shadow looked at Eggman, "What?"

Eggman smiled, "Come, come now Shadow, Rouge, you didn't think that construction bot was the only one I had built."

Rouge tilted her head, "So that's what was making that noise in that office."

Eggman though was too busy thinking to notice Rouge's comment _Of course, I don't really know what that reinforcement is going to be, I never did specify a specific robot for them to build…_.

**With the Museum (Another room):  
**

Ivo sighed as he took another drink of water to calm his nerves, "I can't believe we forgot about the Ambassadors, just imagine what would of happened if we hadn't shown up!"

Shadow smirked from the chair he was lounging on, turning the page of the sports magazine he was reading, "Ivo, you've had us imagine that for the past half-hour. You need to calm down, relax. The last time you were this uptight you ran to the bathroom and threw up as soon as the audience couldn't see you."

Ivo nodded, and sweated, "Your right, but you know how I get when I have to talk to so many people! What if I make a mistake, or trip as I'm walking to the microphone, or…"

Maria put a comforting hand on Ivo's shoulder, "It'll be alright Ivo, you've done this before and nothing has ever happened, this time shouldn't be any different, why don't you practice your speech, you all ways seem to calm down when you do that."

Ivo straightened, "That's it, that's what I'll do, you always know what's needed Maria, I don't know what I'd do without you."

Ivo quickly left the room, Shadow got up from the chair, "You know Maria, he still recites his last speech in his sleep."

Maria smiled, "I guess that's what we get having him practice them constantly, but that's the only thing that calms him enough to go out there, he's always been good at public speaking Shadow but he's also always suffered an extreme case of stage fright before he does."

Shadow smiled, "Don't forget after."

Maria just shook her head at Shadow, smiling, "You really shouldn't make fun of him Shadow."

Shadow shrugs, "I know, but it's the best way to get him to stop thinking about his projects and have some fun, besides, he knows I never really mean any of it."

Maria began to walk towards the door with Shadow, "Are you sure?"

Shadow nodded, "Of course I'm sure, he asked me just last year."

Maria laughed as they left the room.

**Museum's Main Hall:  
**

Arthur quickened his pace as they neared the large crowd in the main hall, a large room with a stage set up at one end and that had a second floor balcony overlooking it. "Come on now, the ceremony's started, the President is about to make her speech!"

Sonic and Tails were confused by this but followed, _I thought the president was a guy!  
_

Cream turned to Amy, "Don't you think this is exciting Ms. Amy"

Amy nodded, "It sure is Cream, but why did you bring your Chao here?"

Cream looked at Cheese then back at Amy, "I never go anywhere without Cheese, he's my best friend."

Tails then came up to them, "Shh, she's starting."

Up front at the podium was the president, Maria, behind her were the Ambassadors in their ceremonial robes guarded by Rouge and their escorts, Ivo, who was just off stage, and Shadow who was hidden by the crowd, "Thank you, now, what all of you here today are about to see is the result of years of diplomacy and fidelity between the Global United Nations and the Echidna peoples. Once again, despite the previous attempted theft of their sacred crystal the Echidna's are donating to us one of their crystals for research into its power. Our scientists believe that if we are able to duplicate that power, we will finally have no more need for heavily polluting or nuclear power plants, and that this clean energy can be provided to all people across the world!"

Cheers rose from the most of the crowd, even Sonic was making an attempt to stand still and listen, but a few people in the crowd didn't, one of which being Ambrosia hidden under a cloak, _That's right Madame president, keep talking as my men move into position._

Maria soon finished her speech and the Echidna Ambassador began his, as he spoke Ambrosia began to move through the crowd towards the podium, what Ambrosia didn't notice was that she was heading straight for Amy.

Once the Ambassador had given his speech and had been given a loud applause Maria stepped up to the podium again, "Now the Head of the Advanced Rescue Command will receive the sacred crystal, bringing us one step closer to true friendship between us!"

With that Ivo stepped out from the side of the stage and approached the Ambassador, the moment Sonic saw him and the 'sacred crystal' he started towards them, _What the? A Chaos Emerald! and what's Eggman doing here? Well whatever it is I'm not letting him get that Chaos Emerald._ Even with his speed Sonic had to move pretty slowly to get through the packed crowd.

That's when chaos ensued.

Ambrosia gave the order to attack then walked right into Amy, her men removed their cloaks and began to fire above the crowd causing everyone to duck, which was the only thing to save the Ambassador's and Rouge's lives as the wall behind them was blown in by Eggman's Egg Walker.

Ambrosia brought out her hammer, while Amy ducked down to with everyone else, Tails quickly grabbed Cream and Arthur and took off and flew them to the floor above, and Sonic stopped in his tracks as ducking crowd revealed Shadow and Rouge, and a second Eggman, Shadow, and Rouge emerged from the smoking hole in the wall, and from his place near the stage, Ambrosia's brother was able to see Sonic quite clearly.?

END CHAPTER 7 OF ALTERATIONS


	8. Fragments of a Shattered Mirror

**SONIC ADVENTURE 2: ALTERATIONS  
**

**DISCLAIMER: **Sonic and the Sonic Adventure series belongs Sega and Sonic Team,  
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.

**Fragments of a Shattered Mirror**

**Museum's Main hall:  
**

Ambrosia was surprised by the explosion, but stood her ground, when most of the smoke had cleared, she signalled her men to aim for the stage, before anyone could speak though a blue hedgehog, eerily like her brother, spoke out, "Eggman!"

Ambrosia turned to that hedgehog, "QUIET YOU FREAK!"

Then Eggman spoke before Ambrosia could continue, "You must be the most persistent living thing I know of Hedgehog, just what will it take to end that existence of yours?"

Ignoring Ambrosia, Sonic answered Eggman, "More than you'll ever be able to throw at me Egg-head."

Throughout this Maria was pulling herself off the floor, "Who are you, and why are you doing this?" she said as she pointed around the main hall.

Ambrosia was the first to answer, "You know why I'm here Madam Presidante, but first I'd like to know who those three are and what they want so that I may decide how to punish them for interfering once I'm done with you."

Eggman smirked, "Your too kind miss, Ambrosia, I believe. Well since you've been so gracious allow me to introduce myself. I, am Doctor Eggman, soon to be recognized as the greatest mind of our times and future ruler of the world! AHAHAHAHAHA!"

Ambrosia smirked as well, "You know I don't see what's so funny, doctor, it's just you and your little pose against my men and possibly that pathetic security guard and the ambassador's men."

(A (only) N: Because it would be too confusing for the readers I'll refer to everyone from Neo-Terra whose name is the same as their Sonic Adventure counterparts as Neo-(insert name here) from here on, do note that this will not apply to speech in between or about characters.)

Neo-Rouge did not like being called pathetic or being referred to as 'security guard' but something big was happening here and she needed to keep a cool head, she whispered to the ambassador, "Ambassador, as soon as there is a chance get yourself out of here, you can take your men but if your only chance is to get out by yourself then take it, my job's to help protect you and nothing is going to stop me from doing it."

In the background Eggman and Ambrosia were arguing, but the Ambassador shook his head, "I'm not what's important here, I'm expendable, the jewel isn't, if I or my men can't get it out I want you to do it, take it either government, I don't care just don't let someone like them get it."

Eggman had had enough, he brought out his laser, "Enough! Now Mr. Ambassador I believe you have something I want, give me the chaos emerald now and I just may spare your life!"

The Ambassador turned to Eggman, "Never, the emeralds will never be used by the likes of you!"

Ambrosia scoffs, "In that case just give it to me, I don't care what you call it, that jewel is the first step to bringing down people like you Doctor, and I'm going to take it! Men, get ready to fire!"

Eggman smirks, "Before they do, I'd like for them to meet the newest addition to MY forces."

With that a shadow appeared in the hole Eggman had made, Ambrosia didn't wait to find out what it was, "Men, fire on his 'Newest addition' then lets see how well he and his companions can impersonate Swiss cheese."

Bullets ricocheted off the shadow as it came through the hole, as it stepped into the light its red and black armour gave off a metallic gleam, it prepared its guns, and fired.

Eggman turned to Rouge and Shadow, "Shadow, Rouge, while there distracted get the Chaos Emerald."

The two nodded, Shadow approached the Ambassador, "I'll take that Emerald now."

Neo-Shadow, on the other hand, wouldn't have anything to do with that and grabbed Shadow's shoulder, "You won't be taking the crystal anywhere."

The battle truly started there, one of Ambrosia's men came too close to Eggman's robot, the machine coldly grabbed the rat's gun and crushed it with its bare hand then punching him in the gut and sending him into a display case.

Shadow grabbed Neo-Shadow's hand a did a summersault and flipped Neo-Shadow over him, even though he was caught off guard, Neo-Shadow was able to land on his feet, Shadow just smirked then took off through the hole into the alley, Sonic saw this and jumped to the stage and followed, as did Neo-Shadow and Neo-Sonic.

Rouge waited until the Ambassador was distracted by Shadow and Neo-Shadow, then grabbed the emerald and took off, Ambassador noticed this immediately, and turned to Neo-Rouge "She's taken the emerald, please you must stop her, The emerald is the only thing that matters!"

Neo-Rouge didn't want to leave the Ambassador, the other one was safe because he had to return home sick, but it was her job to protect him, yet he was insistent that she go, Neo-Rouge bit her lip, then nodded and took flight after the other bat.

Ambrosia was ready to scream, first another blue freak and a Egghead interfere with her plans, then the Egg brings out a robot that's destroying her troops and that 'shadow' with him takes off, presumably with the crystal! Then to her left a young human girl began to cry, the noise began to tear into Ambrosia's mind, the pathetic weakness of it only making her angrier, she turned to the source and brought up her hammer ready to bring it down to end that caterwauling once and for all, "STOP CRYING!!!!"

Amy, from the floor, saw this and knew she had to stop her, acting quickly she brought out her own hammer, "No you don't!"

Ambrosia was caught off guard as a hammer like her own slammed into her side, the force painfully flung her away from her target, yet didn't cause any permanent injury, but once Ambrosia saw the hedgehog who had hit her she scowled and it was clear she wouldn't return the favour.

**Outside the Museum:  
**

Rouge flew over the roofs of the buildings of Station Square, as she did she admired the Chaos Emerald in her hand, the way it sparkled as it caught the light of the city below, then she heard an oddly familiar rustling sound and dodged right as the bat from the Museum attempted to knock her out of the sky, Rouge landed and so did the other bat, "Come on, is that really the best you could do?"

Neo-Rouge answered but felt something was wrong here, the voice this new Thief reminded her of a twisted version of her own, "I wasn't even trying Thief, now return the crystal and maybe the judge will be lenient on your sentencing."

Rouge laughed, "Come on now, you don't really think you're bringing me in do you? Besides, this little Chaos Emerald is such a nice gem, it'd be a waste to see it sitting in the Museum gathering dust."

Neo-Rouge growled, "I don't know why I'm wasting my breath with you thief! Now return the emerald or I'll take it from you by force!"

Rouge smirked, "You and what army?"

Neo-Rouge scowled and ran towards Rouge, when she was within range she jumped and attempted to bring her foot down onto Rouge's head, Rouge dodged and followed with a round-house in an attempt to catch the other bat off guard.

Neo-Rouge just barely escaped it, _What's going on? That's the move I would of made! She's doing everything I'd do, it's like fighting a mirror!_, "Who the heck are you?"

Rouge smiled, "My name, well, if you really want it, the name's Rouge."

**Elsewhere in Station Square:  
**

Neo-Shadow chased Shadow step for step, "Come back here you faker!"

Shadow quickly looked over his shoulder then put his attention back on the road, _I can't believe he just said that!_

Just then Sonic came up to them from the left, "Hey, is this a private party or is anyone invited?"  
  
Shadow smirked, "Still breathing hedgehog? Just what does it take to stop you?"

Sonic laughed, "Nice to see you too."

Neo-Shadow looked at Sonic with surprise, "Who are you?"

Sonic looked at Neo-Shadow and smirked, "Name's Sonic, Sonic the Hedgehog."

Shadow looked at the two and shook his head, "If you're done talking, I've got to run."

As Shadow speed up Neo-Shadow put on speed, "Not without me your not!"

Sonic Speed up too, "Hey, that's my line!"

Behind the trio, Neo-Sonic was struggling to catch up.

END CHAPTER 8 OF ALTERATIONS


	9. Smoke and Mirrors

**SONIC ADVENTURE 2: ALTERATIONS**

DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,  
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.

_******Smoke and Mirrors**_

******Museum's Main Hall:**

Ambrosia was pissed, first the Egg-head ruined her plans, and then this upstart catches her off guard, "You're going to die you B!"

Amy was scared but stood her ground, Sonic had gone after the two Shadows and the Emerald, but she couldn't let her fear stop her from stopping this psychopath from hurting innocent people.

All around the two hedgehogs bullets were fired and ricocheted off there target or bore deep holes into what they hit, not a dent showed on Eggman's latest machination, and Ambrosia's men cared little for the people on the ground. In places on the floor, blood had already began to stain tile, and from the floor above Tails saw one of Ambrosia's men prepare to make a hostage into a living shield from the black/red machine.

As Tails jumped to stop what he saw, Ivo made a drastic move, a gun left lying on the floor by the other ambassador's guard when the two had run in the confusion, taking a chance to stop this he grabbed the gun, and pointed it at Eggman's head, his hands shaking so hard he looked like he was going to drop it.

Eggman noticed, and just grinned as he turned the Egg Walker and moved towards the petrified scientist, Ivo just shook harder, "Stop right there, don't come any farther, just, just leave and take…"

Eggman just laughed, "HOHOHOHO, you think I'm scared of that little peashooter, You've never held a gun in your life have you? HOHOHOHO…" It was at that point that Ivo finally lost his grip on the gun and it fell uselessly to the floor.

Behind them Maria, seeing her cousin in danger and knowing she needed time got off the stage and grabbed a gun off of one of Ambrosia's men that had fallen, her voice was clear and commanding as she pointed the weapon at Eggman, "Stop right there and leave Ivo alone, You have no right to do what you have done, I'm placing you under citizen's arrest, if you don't…"

Having turned to see who was threatening him now, Eggman just laughed harder at Maria's little rant, "HAHAHHAAHHAHHAAHHOHOHHOO, A president that actually has some backbone and morals, I'm impressed madam president, but I…"

Maria's warning shot ricochets off of the right flank of the Egg walker, and Eggman's grin quickly turned into a scowl, where Ivo had no intention or ability to shoot, Maria would and could if it meant protecting her family, her friends, or even others she did not know.

Maria had no intention on missing the second time so long as others were in danger.

******The Echidna Border, "Mystic Ruins":**

Knuckles walked slowly through the jungle as he looked back at the Master Emerald, in the years he had guarded it, he knew it had great power and had to be protected at all costs, but he never really thought about the connection it had to the chaos emeralds as being important, that is, until Chaos appeared and the Emerald shattered.

It was then that Knuckles realized that the powers of the Master Emerald and the Chaos Emeralds were entwined in ways he could not imagine, his people had been destroy… "What the Heck!"

Before Knuckles was a city he had never seen in his life, in the middle of the jungle, where his Island had broken off from the land, a city full of Echidnas.

Then from his right came the sound of running feet and a few distant cries.

**********Somewhere within Station Square:**

Neo-shadow dodged another attack directed at him from his counter-part, the strange blue hedgehog beside him launched his own attack at Shadow while he was distracted, only to stop as another blue hedgehog came up with a knife and prepared to stab Shadow in the back.

Sonic didn't know who's side the second shadow was on, but he was not one to let others get stabbed in the back, he broke off his spin dash and homing attacked the new blue look-alike making it drop the knife, and catching a glimpse of dead emerald eyes, full of despair and loss.

Neo-shadow didn't know what to do, except keep running, and then dodge another of Shadow's attack as he wondered just who this blue hedgehog who saved him is.

**************Another location in Station Square, Rooftops:**

Neo-Rouge sent another kick Rouge's way, her mind split between getting the sacred crystal away from this thief, and why this thief, a practical mirror of herself, would be doing these things.

Rouge easily dodged the attack, since announcing her name her counter-part's fighting had gotten sloppy as she got distracted, if that was all it took to spook her counter part she didn't see why see didn't do it sooner.

Then it was Rouge's distraction that allowed Neo-Rouge to make a grab for the emerald, off guard Rouge noticed but acted to late as her lawful counter-part stole the emerald from her, Rouge cursed under her breath then began to attack herself, now was no longer the time to play around.

******************Back within the Museum:**

Tails jumped as another of Ambrosia's men brought his gun to bear, the hare smirked as he pulled the trigger but the young fox was no longer in the path of his bullets, Tails' tails spun faster, pulling him out of the line of fire, then stopped as he dropped down on the terrorist's head, knocking the hare out cold.

The two men he had stopped lay on the floor, while the young mouse that the first was going for just stared at Tails with some awe.

Above, Cream, Cheese and Arthur did there part with some "Aerial Bombardment", dropping some of the less important items from various displays onto the heads of the targets who had the misfortune of being below them.

It was now, as the battle began to wind down that sirens could be heard.

_******************END CHAPTER 9 OF ALTERATIONS.**_


	10. Heritage, Identity, and Past

**SONIC ADVENTURE 2: ALTERATIONS**

DISCLAIMER: Sonic and the Sonic Adventure series belongs Sega and Sonic Team,  
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.

* * *

**Heritage, Identity, and Past will not be forgot…**

"STOP, THEIF! STOP HIM, HE HAS THE EMERALD!" rang throughout the forest, turning Knuckles saw a figure coming towards him, hooded by a plain brown cloak, hunched over something, that gave him a very familiar feeling. A green flash came from beneath the cloak, and for Knuckles, with years of training bordering now on instinct for the Guardian of the Master Emerald, that was all it took for him to prepare to take this guy down.

The thief, smirking at his prize, hadn't noticed Knuckles on the path ahead of him when had been standing there, but that did not make him stupid. The thief slowed then hid, quietly listening for the guards of that were following him, quietly elated to find that they were going in the wrong direction, till he heard a rustling sound behind him.

Knuckles struck first, the rustle had alerted the thief to prepare for an attack, but like the guards, in the wrong direction. Knuckles came from the side, catching the thief, but not off guard, the thief struck back at Knuckles catching him in the shoulder. The Emerald that the thief had beneath his cloak dropped to the forest floor as they fought, a drop of blood falling behind it.

"HOLD!" The guards had returned, as the thief turned to leave Knuckles caught a glimpse of the face beneath the cloak, his own.

**Station Square:**

As the sirens got louder, more of Ambrosia's that were able seemed to disappear into the shadows, as had Ambrosia herself. She had no desire to get caught, and wasn't fool enough to take on the existing guards and re-enforcements with what she had.

Eggman on the other hand, was more concerned about the president in front of him, he hadn't expected someone like Maria Robotnik to become even remotely violent. He had underestimated what she would do to protect others though, especially family.

Carefully, the mad doctor typed a command into his walker, as he did Maria began to speak, "I don't know who you really are, or why you attacked us today, but I won't let you do any more harm. There are men coming who are more than able to stop you, I'm not going to put this gun down, but I am going to give you one chance, either you give up, or you leave now, either way know that you WILL end up behind bars…"

Once again, Eggman grinned…

******Echidna boarder:**

The Guard behind Knuckles pointed his gun at Knuckles, "You, Stand where you are!"

Knuckles slowly got himself off the ground, he had heard the hammer cock as the Guard aimed his weapon, even he couldn't move or dig fast enough to get away from a bullet at that range.

The Guard then shouted another command, "Now put your hands in the air and turn around!", as Knuckles did he noticed two things, the first was the other guard head over to the Emerald on the ground, the other was the dropping jaw of the Guard with the gun pointing at him.

"Cousin?"…

**********Within Station Square:**

Shadow tired of this little game of "tag", "It's time to end this pointless chase, CHAOS SPEAR!"

Shadow's attack shattered the asphalt in front of Neo-Shadow and Sonic, stopping them in their tracks.

Sonic shielded his face from the debris, "Hey!", this worked exactly as Shadow had planned, "CHAOS CONTROL".

At this, despite knowing full well of the flash to follow, his eyes widened when he heard Shadow called out the technique, _He can't possibly! It's Impossible!_

He did, Shadow disappeared in a flash of green chaotic light, and Neo-Shadow just stared.

Sonic on the other hand, just got annoyed, "I really wish he wouldn't do that, hey where did that other guy go?"

Neo-Shadow just turned his stare to Sonic, "Who are you?"

Sonic just turned towards Neo-Shadow like he had just noticed he was there, "huh? Oh, I'm Sonic, Sonic the Hedgehog.", offering his hand like he would to a friend.

Neo-Shadow carefully took Sonic's hand, shook it gently, yet continued to stare, even after hearing Sonic's reply, _Who is this guy?_

The Sonic did something that really made Neo-Shadow question everything he had ever know, or thought he had known, "Oh man, Tails and Cream! I left them back at the Museum, I gotta get back. Nice to meet you, maybe I'll see you around, now CHAOS CONTROL!"

Neo-Shadow just fell to his knees, _He, He, He used Chaos Control! How did he use Chaos Control! This is INSANE! I must be losing my mind! Just Who is Sonic the Hedgehog?_

Neo-Shadow looked down, then go back up, now was not the time to question, people he considered the closest thing he had to family were in danger, with his questions put on the back burner Neo-Shadow looked back the way he had come, then did as the other two had.

With a quick cry of "Chaos Control", he disappeared as well, while above the fight between to certain bats continued, and far away, some Echidna's were getting the surprises of their lives.

**********_End of Chapter 10 of Alterations._**

**********_Sneak peek: "You look like my nephew but I can tell your not, you haven't fallen as he onto dark paths…"_**


	11. Advent Chaos

**SONIC ADVENTURE 2: ALTERATIONS  
**

**DISCLAIMER: **Sonic and the Sonic Adventure series belongs Sega and Sonic Team,   
if anyone affiliated with the above groups that has a problem or complaint about this fiction it will be dealt with quickly,  
and if they so choose, the story will be deleted.

_**ADVENT CHAOS**_

**Echidna border:**

The Guard's gun almost fell out of his quickly numbing hands, or was it his mind that was numbing, the guard had to lock his knees from falling over, "Knuckles, is… …is that you?"

Knuckles was surprised that this Echidna knew his name, he was even more surprised that he was standing before him. As far as Knuckles knew he was the last of the Echidna's, still the surprise he felt did not show in his face, his training as Guardian would not allow it when he prepared for a fight. "How do you know my name?"

The other Guard came up to the two, confused but not as out of sorts as his partner, "Uh, not to break-up a family reunion or anything but we have to get the Master Emerald back to the Central Control…"

The First Guard then shook his head to clear it, "Right, come on, let's head home" He then noticed Knuckles not following, "Come on Kunx's, I don't know why you left, but lets head home."

Never changing his expression Knuckles began to follow this time, his curiosity about who this Guard really was, and whether that Emerald truly was another Master Emerald, won out over the feeling that something about this entire thing was more then wrong.

**Station Square Museum:  
**

Eggman then laughed, a maniacal whooping sound that made shivers run down Ivo's spine and that Maria found very un-nerving, "Very well Madame President, I think this little distraction has gone on long enough don't you…" Eggman's grin widens as he leans forward, then he turns quickly to his now slightly bloody creation, "Omega, new orders, return to base."

The now named Omega turned his visual sensors to his master then to the guard he had been preparing to throw, the blood from a cut on the guard's head and bleeding nose running over Omega's cold, metallic claws. As if throwing away a scrap of paper, the red and black behemoth idly tosses the guard to the floor then walks out the hole in the wall followed by his master, who left grinning like an insane clown all the way.

While Ivo and Maria watched the mad scientist leave, Maria, never letting the gun-sight leave the back of the mad-man's skull, they did not notice Sonic re-appear on the upper-floor where Cheese, Cream, Arthur, and now Tails stood. "Man, I would have gone to the Museum a long time ago if I knew it'd be this exciting."

Arthur, not really caring where Sonic had appeared from, watched the S.W.A.T. team enter through the front doors then just sat himself down along the balcony's railing, "Exciting indeed, I don't think my heart will ever stop pounding, I'll help with the clean-up downstairs if they let me, why don't you guys head home, I bet your families will be very worried about you all."

That's when Cream realized something, "I forgot! I never told Mom that I was going to the museum! I hope she isn't too worried about me, but I should of called her before I left."

Tails just patted Cream on the back, "It's alright Cream, I'm sure she'll understand, besides Arthur's right, why don't we head home."

Arthur then got himself up, "Well then, why I don't I let you guys out the side entrance, the front is a little crowded right now."

**Somewhere outside of Station Square:  
**

Neo-Sonic stumbled, out of breath and sore, he hadn't run like that since his adoptive parents died, he finally stopped, tears were beginning to well up in his eyes, _I failed, again…_

Neo-Sonic fell to his knees, tears flowing freely down his face, "WHY, WHY CAN'T I do anything right, why?" Sobs racked his body with every breath, his nose beginning to run, when he heard the scuff of someone shifting their weight, a strangely familiar sound for him.

Slowly Neo-Sonic turned around as the setting sun's light glinted off of the stranger's cold metallic mask.

**Ambrosia's Base camp:  
**

Ambrosia was nearly mad with rage, the entire plan had turned into a fiasco, a lot of her men were injured, some were arrested, and fewer still, dead, most by the hands of Eggman's machination.

And where on Neo-Terra was that damned brother of hers, she felt the need to beat him good if he didn't come back with that emerald…

**Echidna Capitol (mystic ruins), Guardian's spire:  
**

The two guards had lead Knuckles through a grand capital city to it's core, a great spire rising higher than any building in Station Square, the guards had lead him in through the front doors.

Inside, Knuckles once again had to rely on his all of his training as Guardian to not let his mouth drop to the floor, within the spire it was like a whole other city, illuminated by a great light near the top of the spire, which the elevator he just entered lead to.

The elevator was surprisingly quick to reach its destination, the doors opening out onto what appeared to be a cross between the Master Emerald's Shrine Knuckles knew so well and a Chao Garden, and there in the standing before a pond encircling a pedestal stood an Echidna that was a spiting image of his ancestor, Tikal's Father, staring across the pond.

The Guard carrying the other Master Emerald walked over to the Echidna, and placed it carefully in his hand, then turned to leave, while the Echidna turned to face Knuckles.

At that instant, Knuckles had no doubt what he was looking at, a guardian of the Master Emerald, but the question of who remained unanswered. As the guards entered the elevator and the doors closed the other guardian walked forward, holding the Emerald in his hand.

Staring Knuckles straight in the eye he spoke, "You look like my nephew but I can tell your not, you haven't fallen as he onto dark paths…", and as he spoke the water rippled, then began to rise and take a shape Knuckles secretly had hoped never to have to lay his eyes upon again.

**Somewhere outside of Station Square:**

Miles Prower looked down upon his un-invited guest, this strange hedgehog had come barreling into his home, an abandoned mine turned scrap-yard that both G.U.N. and Station Square dumped their unwanted trash upon, a place for thing thrown out by civilization and it's society.

Even though the hedgehog was obviously winded, the speed he had in that state was still faster then it should have been, as Prower, un-moved as he was by it's cry into the dying daylight, shifted his weight to get a better look at the intruder, it heard his movement and turned to him, and in it's, no his, eyes Prower saw a pain he knew all to well.


End file.
